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Don't require zarr 3 Bytes Codec configuration key #8282

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Don't require zarr 3 Bytes Codec configuration key #8282

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@frcroth frcroth commented Dec 16, 2024 •
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URL of deployed dev instance (used for testing):

  • https://___.webknossos.xyz

Steps to test:

  • Read a zarr dataset where bytes codec does not have a configuration key

Note that other implemented codecs don't only include optional fields, thus the configuration key is neccessary.

Issues:

(Please delete unneeded items, merge only when none are left open)

  • Updated changelog
  • Needs datastore update after deployment

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coderabbitai bot commented Dec 16, 2024 •
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📝 Walkthrough
📝 Walkthrough

Walkthrough

The changes in the Zarr3ArrayHeader.scala file focus on improving the parsing and handling of Zarr3 array headers, particularly for codecs without explicit configurations. The modifications enhance the robustness of codec reading by introducing more flexible configuration extraction, especially for bytes codecs. The updates ensure that missing or minimal configurations can be processed without causing parsing errors, addressing challenges with different Zarr3 metadata formats.

Changes

File Change Summary
webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr3/Zarr3ArrayHeader.scala - Updated readCodecs method to handle codec configurations more flexibly
- Modified assertValid method to improve data type and codec configuration validation
- Enhanced outerChunkShape method to handle chunk grid configurations more explicitly
CHANGELOG.unreleased.md - Updated to reflect changes in dataset tooltip, terminology, layer name handling, dataset renaming, and various bug fixes related to dataset management and codec handling

Assessment against linked issues

Objective Addressed Explanation
Parse Zarr3 array header with bytes codec without configuration [#8233] ✅
Handle optional codec configuration [#8233] ✅
Support minimal codec metadata [#8233] ✅

Possibly related PRs

Suggested labels

bug, documentation

Suggested reviewers

  • daniel-wer

Poem

🐰 In the realm of Zarr, where data flows free,
A rabbit hops through codec complexity
With Option and tryo, we parse with grace
No configuration left without a trace
Bytes dance smoothly, headers now clear! 🧩

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Reviewing files that changed from the base of the PR and between ec0cbf0 and 71139f0.

📒 Files selected for processing (2)
  • CHANGELOG.unreleased.md (1 hunks)
  • webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr3/Zarr3ArrayHeader.scala (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
  • CHANGELOG.unreleased.md
  • webknossos-datastore/app/com/scalableminds/webknossos/datastore/datareaders/zarr3/Zarr3ArrayHeader.scala

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@frcroth frcroth requested a review from fm3 December 16, 2024 13:36
coderabbitai[bot]
coderabbitai bot reviewed Dec 16, 2024
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Actionable comments posted: 0

🧹 Nitpick comments (1)
CHANGELOG.unreleased.md (1)

31-31: Add a comma for better readability.

The sentence would be clearer with a comma before "making".

- Fixed a bug where in the add remote dataset view the dataset name setting was not in sync with the datasource setting of the advanced tab making the form not submittable.
+ Fixed a bug where in the add remote dataset view the dataset name setting was not in sync with the datasource setting of the advanced tab, making the form not submittable.
🧰 Tools
🪛 LanguageTool

[uncategorized] ~31-~31: A comma might be missing here.
Context: ... the datasource setting of the advanced tab making the form not submittable. [#8245...

(AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)

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📒 Files selected for processing (1)
  • CHANGELOG.unreleased.md (1 hunks)
🧰 Additional context used
🪛 LanguageTool
CHANGELOG.unreleased.md

[uncategorized] ~31-~31: A comma might be missing here.
Context: ... the datasource setting of the advanced tab making the form not submittable. [#8245...

(AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)

🔇 Additional comments (1)
CHANGELOG.unreleased.md (1)

36-36: LGTM! Clear and well-referenced changelog entry.

The entry accurately describes the fix implemented in PR #8282 and follows the changelog format.

fm3
fm3 approved these changes Dec 16, 2024
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LGTM, thanks!

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@fm3 fm3 fm3 approved these changes

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Header of zarr3 array with bytes codec without configuration cannot be parsed
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@frcroth @fm3